Hi all,
thanks for suggestions, indeed I was trying to open coor file using Amber
coordinates rather than restart format.
Stefano
2018-02-22 15:42 GMT+01:00 Carlos Simmerling <carlos.simmerling.gmail.com>:
> make sure you are reading the Amber coordinate file as Amber 7 restart
> format, not as Amber coordinates. The Amber coordinates is for trajectory
> files.
>
> On Wed, Feb 21, 2018 at 7:17 PM, Stefano Guglielmo <
> stefano.guglielmo.unito.it> wrote:
>
>> Dear AMBER users,
>> I generated topology and coordinates for a drug-like molecule using
>> Ambertools 16; all seems to have gone ok, but as I try to open prmtop and
>> prmcrd in VMD the geometry of the molecule is completely altered because
>> VMD reads the first number in prmcrd file (i.e. the number of atoms in the
>> molecule) as a coordinate: manually deleting the number solves the problem
>> of visualization. Is there a workaround different from manually deleting
>> the number of atoms in coord file? Or eventually is it possible to delete
>> the number without encountering any issues?
>> I am using VMD 1.9.3.
>> Thanks in advance
>> Stefano
>>
>> --
>> Stefano GUGLIELMO PhD
>> Assistant Professor of Medicinal Chemistry
>> Department of Drug Science and Technology
>> Via P. Giuria 9
>> 10125 Turin, ITALY
>> ph. +39 (0)11 6707178
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
--
Stefano GUGLIELMO PhD
Assistant Professor of Medicinal Chemistry
Department of Drug Science and Technology
Via P. Giuria 9
10125 Turin, ITALY
ph. +39 (0)11 6707178
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Received on Mon Feb 26 2018 - 17:30:04 PST
